diff --git a/python_app/gui/app_window.py b/python_app/gui/app_window.py
index 95886a3..9545035 100644
--- a/python_app/gui/app_window.py
+++ b/python_app/gui/app_window.py
@@ -127,6 +127,9 @@ class AppWindow(
         self._preprocess_set_name = str(self._gui_defaults.preprocess_dialog.set_name)
         self._preprocess_radar_config_dir = str(self._gui_defaults.preprocess_dialog.radar_config_dir)
         self._preprocess_use_all_radar_configs = bool(self._gui_defaults.preprocess_dialog.use_all_radar_configs)
+        self._preprocess_median_sweep_count = max(
+            1, int(self._gui_defaults.preprocess_dialog.median_sweep_count)
+        )
         self._preprocess_radar_variants: list[RadarConfigVariant] = []
         self._preprocess_radar_scan_summary = RadarConfigScanSummary(
             directory_path=self._preprocess_radar_config_dir,
diff --git a/python_app/gui/controllers/app_window_config/profile_io_mixin.py b/python_app/gui/controllers/app_window_config/profile_io_mixin.py
index 7b00e45..93d64c8 100644
--- a/python_app/gui/controllers/app_window_config/profile_io_mixin.py
+++ b/python_app/gui/controllers/app_window_config/profile_io_mixin.py
@@ -470,6 +470,7 @@ class AppWindowConfigProfileIOMixin:
         self._preprocess_set_name = str(gui_state.preprocess_dialog.set_name)
         self._preprocess_radar_config_dir = str(gui_state.preprocess_dialog.radar_config_dir)
         self._preprocess_use_all_radar_configs = bool(gui_state.preprocess_dialog.use_all_radar_configs)
+        self._preprocess_median_sweep_count = max(1, int(gui_state.preprocess_dialog.median_sweep_count))
         self._apply_history_limit_from_config(config)
         self._gpr_geometry_signature = None
         self._gpr_selected_geometry = None
@@ -487,6 +488,7 @@ class AppWindowConfigProfileIOMixin:
                 self._preprocess_dialog.set_set_name(self._preprocess_set_name)
                 self._preprocess_dialog.set_radar_config_dir(self._preprocess_radar_config_dir)
                 self._preprocess_dialog.set_use_all_radar_configs(self._preprocess_use_all_radar_configs)
+                self._preprocess_dialog.set_median_sweep_count(self._preprocess_median_sweep_count)
                 self._preprocess_dialog.set_selected_sets(self._selected_preprocess_sets, emit_signal=False)
 
         self._apply_initial_radar_limits()
diff --git a/python_app/gui/controllers/app_window_config/state_builders.py b/python_app/gui/controllers/app_window_config/state_builders.py
index aa485c7..b41fc6a 100644
--- a/python_app/gui/controllers/app_window_config/state_builders.py
+++ b/python_app/gui/controllers/app_window_config/state_builders.py
@@ -273,6 +273,12 @@ class AppWindowConfigStateBuildersMixin:
             self._preprocess_use_all_radar_configs = self._preprocess_dialog.use_all_radar_configs()
         return bool(self._preprocess_use_all_radar_configs)
 
+    def _current_preprocess_median_sweep_count(self) -> int:
+        """Return current per-combo median sweep count from the dialog."""
+        if self._preprocess_dialog is not None:
+            self._preprocess_median_sweep_count = self._preprocess_dialog.median_sweep_count()
+        return max(1, int(self._preprocess_median_sweep_count))
+
     def _build_gui_state(self) -> GuiStateModel:
         """Build GUI-only persistent state from current widget values."""
         return GuiStateModel(
@@ -367,6 +373,7 @@ class AppWindowConfigStateBuildersMixin:
                 set_name=self._current_preprocess_set_name(),
                 radar_config_dir=self._current_preprocess_radar_config_dir(),
                 use_all_radar_configs=self._current_preprocess_use_all_radar_configs(),
+                median_sweep_count=self._current_preprocess_median_sweep_count(),
             ),
         )
 
diff --git a/python_app/gui/controllers/app_window_pipeline_mixin.py b/python_app/gui/controllers/app_window_pipeline_mixin.py
index 307b960..15aa44d 100644
--- a/python_app/gui/controllers/app_window_pipeline_mixin.py
+++ b/python_app/gui/controllers/app_window_pipeline_mixin.py
@@ -70,7 +70,7 @@ class AppWindowPipelineMixin:
                     + ", ".join(missing_assets)
                 )
 
-            combo_keys = [ComboKey(input_pos=combo.input, output_pos=combo.output) for combo in config.combos]
+            combo_keys = [ComboKey(input=combo.input, output=combo.output) for combo in config.combos]
             active_preprocess_keys = runtime_preprocess_asset_keys(config)
             preprocess_summary = "; ".join(
                 f"{PREPROCESS_ASSET_SPECS[key].display_name}={preprocess_asset_model(config, key).set_name}"
diff --git a/python_app/gui/controllers/app_window_plot/bscan_plot_mixin.py b/python_app/gui/controllers/app_window_plot/bscan_plot_mixin.py
index a23b273..8d18316 100644
--- a/python_app/gui/controllers/app_window_plot/bscan_plot_mixin.py
+++ b/python_app/gui/controllers/app_window_plot/bscan_plot_mixin.py
@@ -95,7 +95,7 @@ def rebuild_bscan_history_from_results(
 
     for collection in result_tail:
         for block in collection.blocks:
-            key = (block.combo.input_pos, block.combo.output_pos)
+            key = (block.combo.input, block.combo.output)
             for payload in block.payloads:
                 if payload.kind != 1 or payload.processing_name != "bscan":
                     continue
diff --git a/python_app/gui/controllers/app_window_plot/trace_plot_mixin.py b/python_app/gui/controllers/app_window_plot/trace_plot_mixin.py
index 40dc878..48d99c8 100644
--- a/python_app/gui/controllers/app_window_plot/trace_plot_mixin.py
+++ b/python_app/gui/controllers/app_window_plot/trace_plot_mixin.py
@@ -152,7 +152,7 @@ class AppWindowTracePlotMixin:
         x_min = np.inf
         x_max = -np.inf
         for block in collection.blocks:
-            combo_key = (int(block.combo.input_pos), int(block.combo.output_pos))
+            combo_key = (int(block.combo.input), int(block.combo.output))
             if combo_filter is not None and combo_key not in combo_filter:
                 continue
             if combo_key not in combo_colors:
@@ -384,7 +384,7 @@ class AppWindowTracePlotMixin:
             )
             magnitude_plot.addItem(magnitude_curve)
             self._trace_magnitude_curves[
-                (int(trace.combo.input_pos), int(trace.combo.output_pos), 0, "__single_trace__")
+                (int(trace.combo.input), int(trace.combo.output), 0, "__single_trace__")
             ] = magnitude_curve
 
         if show_phase:
@@ -396,7 +396,7 @@ class AppWindowTracePlotMixin:
             )
             phase_plot.addItem(phase_curve)
             self._trace_phase_curves[
-                (int(trace.combo.input_pos), int(trace.combo.output_pos), 0, "__single_trace__")
+                (int(trace.combo.input), int(trace.combo.output), 0, "__single_trace__")
             ] = phase_curve
             phase_plot.setYRange(-180.0, 180.0, padding=0.02)
 
diff --git a/python_app/gui/controllers/app_window_preprocess_mixin.py b/python_app/gui/controllers/app_window_preprocess_mixin.py
index f11ecc7..a27cd69 100644
--- a/python_app/gui/controllers/app_window_preprocess_mixin.py
+++ b/python_app/gui/controllers/app_window_preprocess_mixin.py
@@ -43,7 +43,7 @@ class AppWindowPreprocessMixin:
         for index, trace in enumerate(session.captured_traces(), start=1):
             entries.append(
                 f"{display_name}: {index}/{total_count} | "
-                f"input={trace.combo.input_pos} output={trace.combo.output_pos}"
+                f"input={trace.combo.input} output={trace.combo.output}"
             )
         return entries
 
@@ -134,7 +134,12 @@ class AppWindowPreprocessMixin:
                 f"set={TMP_REFERENCE_SET_NAME}, radar_key={radar_key}"
             )
 
-            radar_key, collection = capture_reference_set(config, TMP_REFERENCE_SET_NAME, self._store)
+            radar_key, collection = capture_reference_set(
+                config,
+                TMP_REFERENCE_SET_NAME,
+                self._store,
+                median_sweep_count=self._preprocess_median_sweep_count,
+            )
             self._selected_preprocess_sets["s21_reference"] = TMP_REFERENCE_SET_NAME
             self._selected_preprocess_radar_key = radar_key
             self._processor_run_signature = None
@@ -176,11 +181,13 @@ class AppWindowPreprocessMixin:
         dialog.set_set_name(self._preprocess_set_name)
         dialog.set_radar_config_dir(self._preprocess_radar_config_dir)
         dialog.set_use_all_radar_configs(self._preprocess_use_all_radar_configs)
+        dialog.set_median_sweep_count(self._preprocess_median_sweep_count)
         dialog.set_selected_sets(self._selected_preprocess_sets, emit_signal=False)
         dialog.refresh_requested.connect(self._refresh_sets)
         dialog.selection_changed.connect(self._on_preprocess_selection_changed)
         dialog.radar_config_dir_changed.connect(self._on_preprocess_radar_config_inputs_changed)
         dialog.multi_radar_option_changed.connect(self._on_preprocess_radar_config_inputs_changed)
+        dialog.median_sweep_count_changed.connect(self._on_preprocess_median_sweep_count_changed)
         dialog.start_sequence_requested.connect(self._start_capture_sequence)
         dialog.capture_next_requested.connect(self._capture_next_combo)
         dialog.capture_all_requested.connect(self._capture_all_remaining)
@@ -206,6 +213,11 @@ class AppWindowPreprocessMixin:
         self._preprocess_use_all_radar_configs = dialog.use_all_radar_configs()
         self._refresh_sets()
 
+    def _on_preprocess_median_sweep_count_changed(self) -> None:
+        """Persist updated per-combo median sweep count from the preprocessing dialog."""
+        dialog = self._ensure_preprocess_dialog()
+        self._preprocess_median_sweep_count = dialog.median_sweep_count()
+
     def _on_preprocess_selection_changed(self) -> None:
         """Persist selected preprocessing set names from dialog."""
         dialog = self._ensure_preprocess_dialog()
@@ -314,17 +326,31 @@ class AppWindowPreprocessMixin:
         try:
             config = self._build_config()
             display_name = preprocess_asset_display_name(kind)
+            median_sweep_count = dialog.median_sweep_count()
+            self._preprocess_median_sweep_count = median_sweep_count
             if self._preprocess_use_all_radar_configs:
-                session = self._build_multi_radar_capture_session(config=config, kind=kind, set_name=set_name)
+                session = self._build_multi_radar_capture_session(
+                    config=config,
+                    kind=kind,
+                    set_name=set_name,
+                    median_sweep_count=median_sweep_count,
+                )
                 radar_summary = (
                     f"radar_variants={session.radar_variant_count()}, "
-                    f"combos={session.state().total_count}"
+                    f"combos={session.state().total_count}, "
+                    f"median_sweep_count={median_sweep_count}"
                 )
             else:
-                session = self._build_single_radar_capture_session(config=config, kind=kind, set_name=set_name)
+                session = self._build_single_radar_capture_session(
+                    config=config,
+                    kind=kind,
+                    set_name=set_name,
+                    median_sweep_count=median_sweep_count,
+                )
                 radar_summary = (
                     f"radar_key={self._radar_key(config)}, "
-                    f"combos={session.state().total_count}"
+                    f"combos={session.state().total_count}, "
+                    f"median_sweep_count={median_sweep_count}"
                 )
 
             session.open()
@@ -431,6 +457,7 @@ class AppWindowPreprocessMixin:
         config,
         kind: str,
         set_name: str,
+        median_sweep_count: int,
     ) -> SequentialCaptureSession:
         """Validate and create the existing single-radar capture session."""
         radar_key = self._radar_key(config)
@@ -438,7 +465,12 @@ class AppWindowPreprocessMixin:
         display_name = preprocess_asset_display_name(kind)
         if set_name in existing_sets:
             raise RuntimeError(f"Set '{set_name}' already exists for {display_name} and cannot be overwritten")
-        return SequentialCaptureSession(config=config, kind=kind, set_name=set_name)
+        return SequentialCaptureSession(
+            config=config,
+            kind=kind,
+            set_name=set_name,
+            median_sweep_count=median_sweep_count,
+        )
 
     def _build_multi_radar_capture_session(
         self,
@@ -446,6 +478,7 @@ class AppWindowPreprocessMixin:
         config,
         kind: str,
         set_name: str,
+        median_sweep_count: int,
     ) -> MultiRadarSequentialCaptureSession:
         """Validate and create the multi-radar capture session."""
         self._refresh_preprocess_radar_variants()
@@ -469,6 +502,7 @@ class AppWindowPreprocessMixin:
             kind=kind,
             set_name=set_name,
             radar_variants=self._preprocess_radar_variants,
+            median_sweep_count=median_sweep_count,
         )
 
     def _capture_next_combo(self) -> None:
@@ -554,8 +588,8 @@ class AppWindowPreprocessMixin:
             extra_details = f" | radar_configs={len(capture_result.traces)}"
         else:
             trace = capture_result
-            input_pos = trace.combo.input_pos
-            output_pos = trace.combo.output_pos
+            input_pos = trace.combo.input
+            output_pos = trace.combo.output
             extra_details = ""
 
         dialog.append_capture_log_entry(
@@ -600,8 +634,8 @@ class AppWindowPreprocessMixin:
                 removed_output = removed_capture.combo.output
                 extra_details = f" | radar_configs={len(removed_capture.traces)}"
             else:
-                removed_input = removed_capture.combo.input_pos
-                removed_output = removed_capture.combo.output_pos
+                removed_input = removed_capture.combo.input
+                removed_output = removed_capture.combo.output
                 extra_details = ""
 
             dialog.set_capture_log_entries(self._capture_log_entries_for_session(session))
diff --git a/python_app/gui/preprocess_dialog.py b/python_app/gui/preprocess_dialog.py
index 5f3ccec..3fc8c29 100644
--- a/python_app/gui/preprocess_dialog.py
+++ b/python_app/gui/preprocess_dialog.py
@@ -17,6 +17,7 @@ from PyQt6.QtWidgets import (
     QPlainTextEdit,
     QPushButton,
     QScrollArea,
+    QSpinBox,
     QVBoxLayout,
     QWidget,
 )
@@ -38,6 +39,7 @@ class PreprocessDialog(QDialog):
     selection_changed = pyqtSignal()
     radar_config_dir_changed = pyqtSignal()
     multi_radar_option_changed = pyqtSignal()
+    median_sweep_count_changed = pyqtSignal()
     start_sequence_requested = pyqtSignal(str)
     capture_next_requested = pyqtSignal()
     capture_all_requested = pyqtSignal()
@@ -50,9 +52,10 @@ class PreprocessDialog(QDialog):
         """Initialize window metadata and compose dialog UI."""
         super().__init__(parent)
         self._set_combos: dict[str, QComboBox] = {}
-        self._preview_plot: pg.PlotWidget | None = None
+        self._amplitude_plot: pg.PlotWidget | None = None
+        self._phase_plot: pg.PlotWidget | None = None
         self._preview_placeholder: QLabel | None = None
-        self._preview_host_layout: QVBoxLayout | None = None
+        self._preview_host_layout: QHBoxLayout | None = None
         self._preview_plot_unavailable = False
         self._init_window()
         self._build_ui()
@@ -102,11 +105,28 @@ class PreprocessDialog(QDialog):
         header_row.addWidget(self._kamil_adc_neutral_sets_button)
         header_row.addWidget(refresh_button)
         layout.addLayout(header_row)
+        layout.addLayout(self._build_median_sweep_row(group))
         layout.addWidget(self._build_radar_config_group(group))
 
         layout.addWidget(self._build_selector_group("S21", VISIBLE_PREPROCESS_ASSET_KEYS, group))
         return group
 
+    def _build_median_sweep_row(self, parent: QGroupBox) -> QHBoxLayout:
+        """Build per-combo median sweep-count selector for capture sessions."""
+        row = QHBoxLayout()
+        self._median_sweep_count_input = QSpinBox(parent)
+        self._median_sweep_count_input.setRange(1, 99)
+        self._median_sweep_count_input.setValue(5)
+        self._median_sweep_count_input.setToolTip(
+            "How many sweeps to capture for each combo. The per-frequency median of all "
+            "sweeps is saved, suppressing single-sweep outliers (e.g. random phase glitches)."
+        )
+        self._median_sweep_count_input.valueChanged.connect(self.median_sweep_count_changed.emit)
+        row.addWidget(QLabel("Sweeps per combo (median)"))
+        row.addWidget(self._median_sweep_count_input)
+        row.addStretch(1)
+        return row
+
     def _build_radar_config_group(self, parent: QGroupBox) -> QGroupBox:
         """Build radar-config directory controls for multi-radar preprocessing."""
         group = QGroupBox("Radar Config Variants", parent)
@@ -221,11 +241,16 @@ class PreprocessDialog(QDialog):
         root_layout.addWidget(self._status_label)
 
     def _build_preview_plot(self, root_layout: QVBoxLayout) -> None:
-        """Build lazy preview host used after each successful capture."""
+        """Build lazy preview host used after each successful capture.
+
+        The host holds a side-by-side amplitude (left) and phase (right) plot
+        pair, created lazily on first capture and replacing a placeholder
+        label when the PyQtGraph build supports it.
+        """
         host = QWidget(self)
-        layout = QVBoxLayout(host)
+        layout = QHBoxLayout(host)
         layout.setContentsMargins(0, 0, 0, 0)
-        layout.setSpacing(0)
+        layout.setSpacing(6)
 
         placeholder = QLabel("Preview will appear after the first successful capture.", host)
         placeholder.setWordWrap(True)
@@ -260,6 +285,15 @@ class PreprocessDialog(QDialog):
         """Update multi-radar capture checkbox state."""
         self._use_all_radar_configs_checkbox.setChecked(bool(enabled))
 
+    def median_sweep_count(self) -> int:
+        """Return configured number of sweeps to median-combine per combo."""
+        return max(1, int(self._median_sweep_count_input.value()))
+
+    def set_median_sweep_count(self, count: int) -> None:
+        """Update per-combo median sweep-count spinbox."""
+        with QSignalBlocker(self._median_sweep_count_input):
+            self._median_sweep_count_input.setValue(max(1, int(count)))
+
     def set_radar_config_summary(
         self,
         *,
@@ -385,40 +419,51 @@ class PreprocessDialog(QDialog):
         self._kamil_adc_neutral_sets_button.setEnabled(bool(visible))
 
     def reset_preview(self) -> None:
-        """Clear preview surface and restore default empty-state text when possible."""
-        if self._preview_plot is not None:
-            self._preview_plot.clear()
-            self._preview_plot.setTitle("")
+        """Clear preview surfaces and restore default empty-state text when possible."""
+        if self._amplitude_plot is not None:
+            self._amplitude_plot.clear()
+        if self._phase_plot is not None:
+            self._phase_plot.clear()
         if self._preview_placeholder is not None:
             self._preview_placeholder.setText("Preview will appear after the first successful capture.")
 
     def draw_last_trace(self, trace: TraceData, title: str, *, channel: str) -> None:
-        """Draw the latest captured sweep trace for the requested channel in dB scale."""
+        """Draw amplitude (dB) and wrapped phase (deg, ±180) panes for the latest capture."""
         samples = trace.s11 if channel == "s11" else trace.s21
         magnitude_db = 20.0 * np.log10(np.maximum(np.abs(samples), 1e-12))
-        if self._ensure_preview_plot():
-            assert self._preview_plot is not None
-            self._preview_plot.clear()
-            self._preview_plot.plot(
+        phase_deg = np.degrees(np.angle(samples))
+
+        if self._ensure_preview_plots():
+            assert self._amplitude_plot is not None
+            assert self._phase_plot is not None
+            self._amplitude_plot.clear()
+            self._amplitude_plot.plot(
                 trace.frequency_hz,
                 magnitude_db,
                 pen=pg.mkPen("#4cc9f0", width=1.8),
             )
+            self._phase_plot.clear()
+            self._phase_plot.plot(
+                trace.frequency_hz,
+                phase_deg,
+                pen=pg.mkPen("#f48c06", width=1.8),
+            )
         elif self._preview_placeholder is not None:
             self._preview_placeholder.setText(
                 f"{title}\n"
-                f"input={trace.combo.input_pos}, output={trace.combo.output_pos}, "
+                f"input={trace.combo.input}, output={trace.combo.output}, "
                 f"points={trace.frequency_hz.size}\n"
                 f"Preview plot is unavailable on this PyQtGraph/PyQt6 build."
             )
+
         combo = trace.combo
         self._status_label.setText(
-            f"{title}: input={combo.input_pos}, output={combo.output_pos}, points={trace.frequency_hz.size}"
+            f"{title}: input={combo.input}, output={combo.output}, points={trace.frequency_hz.size}"
         )
 
-    def _ensure_preview_plot(self) -> bool:
-        """Create preview plot lazily and keep a text fallback when unavailable."""
-        if self._preview_plot is not None:
+    def _ensure_preview_plots(self) -> bool:
+        """Create the amplitude+phase plot pair lazily on first successful capture."""
+        if self._amplitude_plot is not None and self._phase_plot is not None:
             return True
         if self._preview_plot_unavailable:
             return False
@@ -426,11 +471,8 @@ class PreprocessDialog(QDialog):
             return False
 
         try:
-            plot = pg.PlotWidget(background="#101418", enableMenu=False)
-            plot.showGrid(x=True, y=True, alpha=0.2)
-            plot.setLabel("bottom", "Frequency", units="Hz")
-            plot.setLabel("left", "Magnitude", units="dB")
-            plot.setMinimumHeight(320)
+            amplitude_plot = self._build_preview_axis("Magnitude", "dB")
+            phase_plot = self._build_preview_axis("Phase", "deg")
         except Exception:
             self._preview_plot_unavailable = True
             return False
@@ -440,10 +482,22 @@ class PreprocessDialog(QDialog):
             self._preview_placeholder.deleteLater()
             self._preview_placeholder = None
 
-        self._preview_plot = plot
-        self._preview_host_layout.addWidget(plot)
+        self._amplitude_plot = amplitude_plot
+        self._phase_plot = phase_plot
+        self._preview_host_layout.addWidget(amplitude_plot, stretch=1)
+        self._preview_host_layout.addWidget(phase_plot, stretch=1)
         return True
 
+    @staticmethod
+    def _build_preview_axis(left_label: str, left_units: str) -> "pg.PlotWidget":
+        """Return one PlotWidget configured with the project's preview style."""
+        plot = pg.PlotWidget(background="#101418", enableMenu=False)
+        plot.showGrid(x=True, y=True, alpha=0.2)
+        plot.setLabel("bottom", "Frequency", units="Hz")
+        plot.setLabel("left", left_label, units=left_units)
+        plot.setMinimumHeight(320)
+        return plot
+
     def _emit_selection_changed(self) -> None:
         """Emit current selection snapshot change."""
         self.selection_changed.emit()
diff --git a/python_app/hardware_full/librevna_multi_device_driver/controller.py b/python_app/hardware_full/librevna_multi_device_driver/controller.py
index 8b2257c..22c1e23 100644
--- a/python_app/hardware_full/librevna_multi_device_driver/controller.py
+++ b/python_app/hardware_full/librevna_multi_device_driver/controller.py
@@ -5,6 +5,7 @@ from __future__ import annotations
 from collections.abc import Iterator, Sequence
 from dataclasses import replace
 from typing import Optional
+import threading
 import time
 
 from python_app.hardware_full.librevna_multi_device_driver.cycle_collection import (
@@ -85,7 +86,17 @@ class MultiDeviceVnaController:
         *,
         master_stimulus_ports: Sequence[int] = (1, 2),
     ) -> None:
-        """Apply reference/sweep settings and leave devices sweeping."""
+        """Apply reference/sweep settings and leave devices sweeping.
+
+        When the requested configuration already matches the running sweep,
+        the host-side packet queues are drained and the device sweep is
+        left untouched, so back-to-back acquires do not pay the SET_IDLE +
+        SWEEP_SETTINGS round-trip cost. The drain is performed in parallel
+        across devices to keep the cross-device timing skew below the USB
+        latency variance, which is what previously let a hardware cycle
+        wrap slip between master and slave drains and desynchronise the
+        per-device cycle counters.
+        """
         if self._is_closed:
             raise RuntimeError("Controller is already closed")
         stimulus_ports = self._normalize_master_stimulus_ports(master_stimulus_ports)
@@ -93,12 +104,6 @@ class MultiDeviceVnaController:
         if not self._reference_configuration_applied:
             self._configure_reference_clocks()
 
-        # Even when the device-side configuration matches and we skip reconfiguration,
-        # the host-side packet queue has been accumulating datapoints from cycles that
-        # ran between calls. Draining here guarantees the next collect_running_sweep_cycles
-        # returns a freshly-arriving cycle (the cycle tracker waits for point_index==0).
-        # Without this drain, callers would receive whichever stale cycle happened to be
-        # at the head of the queue — e.g. data from before a manual cable swap.
         self._drain_all_received_packets()
 
         if (
@@ -111,6 +116,10 @@ class MultiDeviceVnaController:
         if self._sweep_is_running:
             self._send_idle_to_all_devices()
             time.sleep(self._reconfigure_delay_s)
+            # The old sweep keeps streaming datapoints until each device
+            # processes SET_IDLE. Drain again after the idle settling delay
+            # so the new sweep starts on an empty queue.
+            self._drain_all_received_packets()
 
         self._configure_sweep_on_all_devices(
             sweep_configuration,
@@ -192,12 +201,16 @@ class MultiDeviceVnaController:
             pass
 
     def _send_idle_to_all_devices(self) -> None:
+        # SET_IDLE is a one-shot stop command. The ACK may be delayed only by the
+        # in-flight datapoint queue, which drains within a few hundred ms. A short,
+        # single-shot timeout keeps recovery snappy when one device stops responding
+        # so callers (e.g. multi-radar capture) do not block for minutes on retries.
         for device_connection in self._all_devices:
             self._try_send_command_without_failing(
                 device_connection,
                 PacketType.SET_IDLE,
-                timeout_seconds=3.0,
-                retry_count=1,
+                timeout_seconds=1.0,
+                retry_count=0,
             )
         self._sweep_is_running = False
 
@@ -245,8 +258,30 @@ class MultiDeviceVnaController:
         self._sweep_is_running = True
 
     def _drain_all_received_packets(self) -> None:
-        for device_connection in self._all_devices:
-            device_connection.drain_received_packets()
+        # Drain every device queue in parallel rather than one after another:
+        # serial drain leaves up to a few hundred microseconds of skew between
+        # the master and slave drain moments, which is enough room for a
+        # hardware cycle wrap to slip between drains and desynchronise the
+        # per-device cycle counters. Each device has its own queue and lock,
+        # so concurrent get_nowait calls do not contend. A single device case
+        # just runs inline to avoid the thread-spawn overhead.
+        if len(self._all_devices) < 2:
+            for device_connection in self._all_devices:
+                device_connection.drain_received_packets()
+            return
+
+        drain_threads = [
+            threading.Thread(
+                target=device_connection.drain_received_packets,
+                name=f"drain-{device_connection.serial_number}",
+                daemon=True,
+            )
+            for device_connection in self._all_devices
+        ]
+        for drain_thread in drain_threads:
+            drain_thread.start()
+        for drain_thread in drain_threads:
+            drain_thread.join()
 
     @staticmethod
     def _normalize_master_stimulus_ports(master_stimulus_ports: Sequence[int]) -> tuple[int, ...]:
diff --git a/python_app/hardware_full/librevna_multi_device_driver/cycle_collection.py b/python_app/hardware_full/librevna_multi_device_driver/cycle_collection.py
index 0030cfd..a0f2b1b 100644
--- a/python_app/hardware_full/librevna_multi_device_driver/cycle_collection.py
+++ b/python_app/hardware_full/librevna_multi_device_driver/cycle_collection.py
@@ -69,6 +69,13 @@ def collect_complete_running_sweep_cycles(
     else:
         datapoint_timeout_seconds = max(0.5, float(datapoint_timeout_seconds))
 
+    # Upper bound on how long we wait for the first cycle-start datapoint
+    # (point_index==0). Without it, a device that keeps streaming non-zero
+    # indices but never wraps (e.g. after a misconfigured sweep restart)
+    # would refresh `last_datapoint_timestamp` on every incoming packet and
+    # stall capture indefinitely.
+    cycle_start_guard_seconds = max(2.0, datapoint_timeout_seconds * 4.0)
+
     def collect_datapoints_from_device(
         device_connection: LibreVnaUsbBulkConnection,
         handle_datapoint: Callable[[ParsedVnaDatapoint], bool],
@@ -76,12 +83,15 @@ def collect_complete_running_sweep_cycles(
         datapoints_received = 0
         expected_datapoint_count = cycle_count * point_count
         last_datapoint_timestamp = time.monotonic()
+        collection_loop_start = last_datapoint_timestamp
+        has_consumed_any_datapoint = False
 
         while datapoints_received < expected_datapoint_count:
             if stop_collection_requested.is_set():
                 return
 
-            remaining_timeout_seconds = (last_datapoint_timestamp + datapoint_timeout_seconds) - time.monotonic()
+            now = time.monotonic()
+            remaining_timeout_seconds = (last_datapoint_timestamp + datapoint_timeout_seconds) - now
             if remaining_timeout_seconds <= 0:
                 collection_errors.append(
                     TimeoutError(
@@ -93,6 +103,17 @@ def collect_complete_running_sweep_cycles(
                 stop_collection_requested.set()
                 return
 
+            if not has_consumed_any_datapoint and (now - collection_loop_start) > cycle_start_guard_seconds:
+                collection_errors.append(
+                    TimeoutError(
+                        f"Device {device_connection.serial_number} streamed datapoints but never "
+                        f"reached point_index=0 within {cycle_start_guard_seconds:.1f} s "
+                        f"(sweep cycle did not restart)"
+                    )
+                )
+                stop_collection_requested.set()
+                return
+
             try:
                 packet_type, payload = device_connection.receive_packet(
                     timeout_seconds=min(1.0, remaining_timeout_seconds)
@@ -118,35 +139,41 @@ def collect_complete_running_sweep_cycles(
                 last_datapoint_timestamp = time.monotonic()
                 datapoint_was_consumed = handle_datapoint(parsed_datapoint)
                 if datapoint_was_consumed:
+                    has_consumed_any_datapoint = True
                     datapoint_counts_by_device_serial[device_connection.serial_number] += 1
                     datapoints_received += 1
 
     def build_cycle_tracking_handler(
         cycle_aware_handler: Callable[[ParsedVnaDatapoint, int], None],
     ) -> Callable[[ParsedVnaDatapoint], bool]:
+        # The controller restarts the sweep before every collection, so the
+        # first packet each device emits is point 0 of a brand-new cycle 0.
+        # Anchoring cycle 0 on the first observed point_index==0 — instead of
+        # synthesising it from a wrap — pins master and slave threads to the
+        # same physical cycle even if a stale straggler from the just-stopped
+        # sweep escaped the post-idle drain: such a straggler always carries
+        # a non-zero point_index and is discarded until the genuine cycle 0
+        # arrives. From that anchor, each subsequent wrap advances the cycle
+        # counter normally.
         cycle_tracking_state = {
             "current_cycle_index": 0,
             "previous_point_index": -1,
-            "has_seen_cycle_start": False,
+            "synchronized": False,
         }
 
         def handle_datapoint(parsed_datapoint: ParsedVnaDatapoint) -> bool:
             current_point_index = parsed_datapoint.point_index
-            if not cycle_tracking_state["has_seen_cycle_start"]:
+
+            if not cycle_tracking_state["synchronized"]:
                 if current_point_index != 0:
-                    cycle_tracking_state["previous_point_index"] = current_point_index
                     return False
-                cycle_tracking_state["has_seen_cycle_start"] = True
+                cycle_tracking_state["synchronized"] = True
                 cycle_tracking_state["previous_point_index"] = current_point_index
                 cycle_aware_handler(parsed_datapoint, 0)
                 return True
 
-            if (
-                cycle_tracking_state["previous_point_index"] >= 0
-                and current_point_index < cycle_tracking_state["previous_point_index"]
-            ):
+            if current_point_index < cycle_tracking_state["previous_point_index"]:
                 cycle_tracking_state["current_cycle_index"] += 1
-
             cycle_tracking_state["previous_point_index"] = current_point_index
             current_cycle_index = cycle_tracking_state["current_cycle_index"]
             if current_cycle_index >= cycle_count:
diff --git a/python_app/hardware_full/multi_device_service.py b/python_app/hardware_full/multi_device_service.py
index b0dd3d2..100d14c 100644
--- a/python_app/hardware_full/multi_device_service.py
+++ b/python_app/hardware_full/multi_device_service.py
@@ -163,7 +163,7 @@ class MultiDeviceLibreVnaService:
             for input_pos, s_parameter_name in enumerate(_INPUT_S_PARAMETERS_BY_OUTPUT[output_pos]):
                 traces.append(
                     TraceData(
-                        combo=ComboKey(input_pos=input_pos, output_pos=output_pos),
+                        combo=ComboKey(input=input_pos, output=output_pos),
                         frequency_hz=frequencies,
                         s11=reflection,
                         s21=self._required_s_parameter(normalized_s_parameters, s_parameter_name),
@@ -200,7 +200,7 @@ class MultiDeviceLibreVnaService:
                 s21 = (gain * np.cos(phase) + 1j * gain * np.sin(phase)).astype(np.complex64)
                 traces.append(
                     TraceData(
-                        combo=ComboKey(input_pos=input_pos, output_pos=output_pos),
+                        combo=ComboKey(input=input_pos, output=output_pos),
                         frequency_hz=frequencies,
                         s11=s11,
                         s21=s21,
diff --git a/python_app/models/dataset_model.py b/python_app/models/dataset_model.py
index 69f13dd..bfe27d8 100644
--- a/python_app/models/dataset_model.py
+++ b/python_app/models/dataset_model.py
@@ -26,8 +26,8 @@ def _empty_f32_matrix() -> np.ndarray:
 class ComboKey:
     """Switch combination key: input position + output position."""
 
-    input_pos: int
-    output_pos: int
+    input: int
+    output: int
 
 
 @dataclass(slots=True)
diff --git a/python_app/models/gui_profile_codec.py b/python_app/models/gui_profile_codec.py
index 7df9820..5d3a142 100644
--- a/python_app/models/gui_profile_codec.py
+++ b/python_app/models/gui_profile_codec.py
@@ -471,6 +471,15 @@ def gui_profile_from_dict(payload: dict[str, Any]) -> GuiProfileModel:
             gui.preprocess_dialog.use_all_radar_configs,
             "gui.preprocess_dialog",
         ),
+        median_sweep_count=max(
+            1,
+            _optional_int(
+                preprocess_dialog_object,
+                "median_sweep_count",
+                gui.preprocess_dialog.median_sweep_count,
+                "gui.preprocess_dialog",
+            ),
+        ),
     )
 
     profile.gui = gui
@@ -564,6 +573,7 @@ def gui_profile_to_dict(model: GuiProfileModel) -> dict[str, Any]:
             "set_name": gui.preprocess_dialog.set_name,
             "radar_config_dir": gui.preprocess_dialog.radar_config_dir,
             "use_all_radar_configs": gui.preprocess_dialog.use_all_radar_configs,
+            "median_sweep_count": gui.preprocess_dialog.median_sweep_count,
         },
     }
     return payload
diff --git a/python_app/models/gui_profile_schema.py b/python_app/models/gui_profile_schema.py
index 0d5ab2b..646459f 100644
--- a/python_app/models/gui_profile_schema.py
+++ b/python_app/models/gui_profile_schema.py
@@ -127,6 +127,7 @@ class GuiPreprocessDialogStateModel:
     set_name: str = "set_001"
     radar_config_dir: str = ""
     use_all_radar_configs: bool = False
+    median_sweep_count: int = 5
 
 
 @dataclass(slots=True)
diff --git a/python_app/orchestration/shm/decoder.py b/python_app/orchestration/shm/decoder.py
index 0f721ab..2ca1fec 100644
--- a/python_app/orchestration/shm/decoder.py
+++ b/python_app/orchestration/shm/decoder.py
@@ -47,7 +47,7 @@ def decode_trace_collection(payload: bytes, expected_magic: int) -> SweepCollect
 
         traces.append(
             TraceData(
-                combo=ComboKey(input_pos=input_pos, output_pos=output_pos),
+                combo=ComboKey(input=input_pos, output=output_pos),
                 frequency_hz=freq,
                 s11=s11,
                 s21=s21,
@@ -155,7 +155,7 @@ def decode_result_collection(payload: bytes) -> ResultCollection:
 
         blocks.append(
             ResultBlock(
-                combo=ComboKey(input_pos=input_pos, output_pos=output_pos),
+                combo=ComboKey(input=input_pos, output=output_pos),
                 payloads=payloads,
             )
         )
diff --git a/python_app/scripts/convert_legacy_preprocess_sets.py b/python_app/scripts/convert_legacy_preprocess_sets.py
index 71102bf..ba297ae 100644
--- a/python_app/scripts/convert_legacy_preprocess_sets.py
+++ b/python_app/scripts/convert_legacy_preprocess_sets.py
@@ -124,7 +124,7 @@ def _load_legacy_collection(meta_path: Path, npz_path: Path, *, target_kind: str
 
             traces.append(
                 TraceData(
-                    combo=ComboKey(input_pos=input_pos, output_pos=output_pos),
+                    combo=ComboKey(input=input_pos, output=output_pos),
                     frequency_hz=frequency_hz,
                     s11=s11,
                     s21=s21,
diff --git a/python_app/scripts/hardware_raw_orchestrator_test.py b/python_app/scripts/hardware_raw_orchestrator_test.py
index d2ffe60..a06557e 100644
--- a/python_app/scripts/hardware_raw_orchestrator_test.py
+++ b/python_app/scripts/hardware_raw_orchestrator_test.py
@@ -238,7 +238,7 @@ class RawOrchestratorViewer(QMainWindow):
 
         for idx, trace in enumerate(collection.traces):
             magnitude_db = 20.0 * np.log10(np.maximum(np.abs(trace.s21), 1e-12))
-            label = f"input={trace.combo.input_pos}, output={trace.combo.output_pos}"
+            label = f"input={trace.combo.input}, output={trace.combo.output}"
             self._plot.plot(
                 trace.frequency_hz,
                 magnitude_db,
diff --git a/python_app/scripts/kamil_adc_raw_producer.py b/python_app/scripts/kamil_adc_raw_producer.py
index 021d336..d20fed0 100644
--- a/python_app/scripts/kamil_adc_raw_producer.py
+++ b/python_app/scripts/kamil_adc_raw_producer.py
@@ -79,7 +79,7 @@ def main() -> int:
                 sweep = radar.acquire()
                 traces.append(
                     TraceData(
-                        combo=ComboKey(input_pos=combo.input, output_pos=combo.output),
+                        combo=ComboKey(input=combo.input, output=combo.output),
                         frequency_hz=np.asarray(sweep.x, dtype=np.float32),
                         s11=np.asarray(sweep.trace("s11"), dtype=np.complex64),
                         s21=np.asarray(sweep.trace("s21"), dtype=np.complex64),
diff --git a/python_app/scripts/manual_smoke_run.py b/python_app/scripts/manual_smoke_run.py
index cf34cc1..f4488dd 100644
--- a/python_app/scripts/manual_smoke_run.py
+++ b/python_app/scripts/manual_smoke_run.py
@@ -74,7 +74,7 @@ def build_synthetic_collection(
 
         traces.append(
             TraceData(
-                combo=ComboKey(input_pos=combo.input, output_pos=combo.output),
+                combo=ComboKey(input=combo.input, output=combo.output),
                 frequency_hz=frequency_hz,
                 s11=s11,
                 s21=s21,
diff --git a/python_app/storage/npz/serialize.py b/python_app/storage/npz/serialize.py
index b9f4bd0..a0097bb 100644
--- a/python_app/storage/npz/serialize.py
+++ b/python_app/storage/npz/serialize.py
@@ -35,7 +35,7 @@ def serialize_trace_collection(collection: SweepCollection, magic: int) -> bytes
         if freq.size != s21.size:
             raise ValueError("Trace frequency and S21 sizes must match")
 
-        buffer.extend(struct.pack("<III", trace.combo.input_pos, trace.combo.output_pos, int(freq.size)))
+        buffer.extend(struct.pack("<III", trace.combo.input, trace.combo.output, int(freq.size)))
         buffer.extend(freq.astype("<f4", copy=False).tobytes())
 
         _write_interleaved_complex(buffer, s11)
@@ -122,7 +122,7 @@ def serialize_result_collection(collection: ResultCollection) -> bytes:
         serialize_payload(buffer, payload)
 
     for block in collection.blocks:
-        buffer.extend(struct.pack("<II", block.combo.input_pos, block.combo.output_pos))
+        buffer.extend(struct.pack("<II", block.combo.input, block.combo.output))
         buffer.extend(struct.pack("<I", len(block.payloads)))
 
         for payload in block.payloads:
diff --git a/python_app/storage/npz/snapshot_numpy.py b/python_app/storage/npz/snapshot_numpy.py
index 23ba865..6476df3 100644
--- a/python_app/storage/npz/snapshot_numpy.py
+++ b/python_app/storage/npz/snapshot_numpy.py
@@ -157,7 +157,7 @@ def save_trace_history_numpy(stage_dir: Path, history: list[SweepCollection]) ->
 
         traces_meta: list[dict[str, int | str]] = []
         for trace in collection.traces:
-            tag = f"i{trace.combo.input_pos}_o{trace.combo.output_pos}"
+            tag = f"i{trace.combo.input}_o{trace.combo.output}"
             freq = np.asarray(trace.frequency_hz, dtype=np.float32)
             s11 = np.asarray(trace.s11, dtype=np.complex64)
             s21 = np.asarray(trace.s21, dtype=np.complex64)
@@ -166,8 +166,8 @@ def save_trace_history_numpy(stage_dir: Path, history: list[SweepCollection]) ->
             np.save(collection_dir / f"{tag}_s21.npy", s21)
             traces_meta.append(
                 {
-                    "input": int(trace.combo.input_pos),
-                    "output": int(trace.combo.output_pos),
+                    "input": int(trace.combo.input),
+                    "output": int(trace.combo.output),
                     "points": int(freq.size),
                     "freq_file": f"{tag}_freq.npy",
                     "s11_file": f"{tag}_s11.npy",
@@ -260,7 +260,7 @@ def save_result_history_numpy(stage_dir: Path, history: list[ResultCollection])
 
         blocks_meta: list[dict[str, int | str | list[dict[str, int | str | float]]]] = []
         for block_index, block in enumerate(collection.blocks):
-            block_dir = collection_dir / f"block_{block_index:03d}_i{block.combo.input_pos}_o{block.combo.output_pos}"
+            block_dir = collection_dir / f"block_{block_index:03d}_i{block.combo.input}_o{block.combo.output}"
             block_dir.mkdir(parents=True, exist_ok=False)
 
             payload_meta: list[dict[str, int | str | float]] = []
@@ -325,8 +325,8 @@ def save_result_history_numpy(stage_dir: Path, history: list[ResultCollection])
 
             blocks_meta.append(
                 {
-                    "input": int(block.combo.input_pos),
-                    "output": int(block.combo.output_pos),
+                    "input": int(block.combo.input),
+                    "output": int(block.combo.output),
                     "payload_count": len(block.payloads),
                     "dir": block_dir.name,
                     "payloads": payload_meta,
diff --git a/python_app/storage/npz/store.py b/python_app/storage/npz/store.py
index b679179..7e5789c 100644
--- a/python_app/storage/npz/store.py
+++ b/python_app/storage/npz/store.py
@@ -48,7 +48,7 @@ class NpzStore(StoreApi):
         combo_records: list[dict[str, str | int]] = []
 
         for trace in collection.traces:
-            suffix = f"i{trace.combo.input_pos}_o{trace.combo.output_pos}"
+            suffix = f"i{trace.combo.input}_o{trace.combo.output}"
             freq_key = f"freq_{suffix}"
             s11_key = f"s11_{suffix}"
             s21_key = f"s21_{suffix}"
@@ -57,8 +57,8 @@ class NpzStore(StoreApi):
             payload[s21_key] = np.asarray(trace.s21, dtype=np.complex64)
             combo_records.append(
                 {
-                    "input": trace.combo.input_pos,
-                    "output": trace.combo.output_pos,
+                    "input": trace.combo.input,
+                    "output": trace.combo.output,
                     "freq_key": freq_key,
                     "s11_key": s11_key,
                     "s21_key": s21_key,
@@ -94,7 +94,7 @@ class NpzStore(StoreApi):
             s21 = np.asarray(arrays[combo["s21_key"]], dtype=np.complex64)
             traces.append(
                 TraceData(
-                    combo=ComboKey(input_pos=int(combo["input"]), output_pos=int(combo["output"])),
+                    combo=ComboKey(input=int(combo["input"]), output=int(combo["output"])),
                     frequency_hz=freq,
                     s11=s11,
                     s21=s21,
@@ -119,8 +119,8 @@ class NpzStore(StoreApi):
     def has_combo_coverage(self, kind: str, radar_key: str, set_name: str, combos: list[ComboKey]) -> bool:
         """Validate that named set covers all required switch combinations."""
         collection = self.load_set(kind, radar_key, set_name)
-        existing = {(trace.combo.input_pos, trace.combo.output_pos) for trace in collection.traces}
-        required = {(combo.input_pos, combo.output_pos) for combo in combos}
+        existing = {(trace.combo.input, trace.combo.output) for trace in collection.traces}
+        required = {(combo.input, combo.output) for combo in combos}
         return required.issubset(existing)
 
     def export_set_bundle(self, kind: str, radar_key: str, set_name: str, output_path: Path) -> Path:
@@ -295,7 +295,7 @@ class NpzStore(StoreApi):
 
         combos = sorted(
             {
-                (int(trace.combo.input_pos), int(trace.combo.output_pos))
+                (int(trace.combo.input), int(trace.combo.output))
                 for collection in [*selected_raw, *selected_preprocessed]
                 for trace in collection.traces
             }
diff --git a/python_app/storage/npz/vna_history_json.py b/python_app/storage/npz/vna_history_json.py
index d311ece..a147b3e 100644
--- a/python_app/storage/npz/vna_history_json.py
+++ b/python_app/storage/npz/vna_history_json.py
@@ -39,7 +39,7 @@ def _select_trace_samples(trace: TraceData, channel: str) -> np.ndarray:
 
 def _pick_trace(collection: SweepCollection, input_index: int, output_index: int) -> TraceData | None:
     for trace in collection.traces:
-        if int(trace.combo.input_pos) == int(input_index) and int(trace.combo.output_pos) == int(output_index):
+        if int(trace.combo.input) == int(input_index) and int(trace.combo.output) == int(output_index):
             return trace
     return None
 
diff --git a/python_app/tests/test_kamil_adc_neutral_preprocess.py b/python_app/tests/test_kamil_adc_neutral_preprocess.py
index cbc1c57..c965252 100644
--- a/python_app/tests/test_kamil_adc_neutral_preprocess.py
+++ b/python_app/tests/test_kamil_adc_neutral_preprocess.py
@@ -42,7 +42,7 @@ class KamilAdcNeutralPreprocessTest(unittest.TestCase):
         self.assertEqual(len(calibration.traces), 2)
         self.assertEqual(len(reference.traces), 2)
         self.assertEqual(
-            [(trace.combo.input_pos, trace.combo.output_pos) for trace in calibration.traces],
+            [(trace.combo.input, trace.combo.output) for trace in calibration.traces],
             [(0, 0), (1, 0)],
         )
         for trace in calibration.traces:
diff --git a/python_app/workflows/calibration_workflow.py b/python_app/workflows/calibration_workflow.py
index b8c9c90..d1a824b 100644
--- a/python_app/workflows/calibration_workflow.py
+++ b/python_app/workflows/calibration_workflow.py
@@ -5,13 +5,18 @@ from __future__ import annotations
 from python_app.models.dataset_model import SweepCollection
 from python_app.models.run_config_model import RunConfigModel
 from python_app.storage.npz_store import NpzStore
-from python_app.workflows.sequential_capture_workflow import SequentialCaptureSession
+from python_app.workflows.sequential_capture_workflow import (
+    DEFAULT_CALIBRATION_MEDIAN_SWEEP_COUNT,
+    SequentialCaptureSession,
+)
 
 
 def capture_calibration_set(
     config: RunConfigModel,
     set_name: str,
     store: NpzStore,
+    *,
+    median_sweep_count: int = DEFAULT_CALIBRATION_MEDIAN_SWEEP_COUNT,
 ) -> tuple[str, SweepCollection]:
     """Capture all switch combinations and persist them as calibration set."""
     if config.is_multi_device:
@@ -21,7 +26,12 @@ def capture_calibration_set(
             "and captured explicitly."
         )
 
-    session = SequentialCaptureSession(config=config, kind="s21_calibration", set_name=set_name)
+    session = SequentialCaptureSession(
+        config=config,
+        kind="s21_calibration",
+        set_name=set_name,
+        median_sweep_count=median_sweep_count,
+    )
     try:
         session.open()
         while not session.is_complete():
diff --git a/python_app/workflows/kamil_adc_neutral_preprocess.py b/python_app/workflows/kamil_adc_neutral_preprocess.py
index 72efd24..a6015cc 100644
--- a/python_app/workflows/kamil_adc_neutral_preprocess.py
+++ b/python_app/workflows/kamil_adc_neutral_preprocess.py
@@ -62,7 +62,7 @@ def _neutral_collection(
         point_count = int(frequency_hz.size)
         traces.append(
             TraceData(
-                combo=ComboKey(input_pos=int(combo.input), output_pos=int(combo.output)),
+                combo=ComboKey(input=int(combo.input), output=int(combo.output)),
                 frequency_hz=frequency_hz.copy(),
                 s11=np.zeros(point_count, dtype=np.complex64),
                 s21=np.full(point_count, s21_value, dtype=np.complex64),
diff --git a/python_app/workflows/multi_radar_capture_workflow.py b/python_app/workflows/multi_radar_capture_workflow.py
index b3f2e68..9bf29ae 100644
--- a/python_app/workflows/multi_radar_capture_workflow.py
+++ b/python_app/workflows/multi_radar_capture_workflow.py
@@ -18,6 +18,8 @@ from python_app.workflows.radar_config_variants import RadarConfigVariant
 from python_app.workflows.sequential_capture_workflow import (
     MULTI_DEVICE_MANUAL_CAPTURE_KINDS,
     SequentialCaptureState,
+    combine_collections_via_median,
+    combine_traces_via_median,
     select_trace_for_combo,
 )
 
@@ -55,6 +57,7 @@ class MultiRadarSequentialCaptureSession:
         kind: str,
         set_name: str,
         radar_variants: list[RadarConfigVariant],
+        median_sweep_count: int = 1,
     ) -> None:
         """Create capture session for one preprocess asset set and multiple radar variants."""
         if kind not in {"s21_calibration", "s21_reference", "s11_open", "s11_short", "s11_load", "s11_reference"}:
@@ -63,11 +66,14 @@ class MultiRadarSequentialCaptureSession:
             raise RuntimeError("Set name is required")
         if not radar_variants:
             raise RuntimeError("At least one radar variant is required")
+        if int(median_sweep_count) < 1:
+            raise RuntimeError("median_sweep_count must be >= 1")
 
         self._base_config = base_config
         self._kind = kind
         self._set_name = set_name
         self._radar_variants = list(radar_variants)
+        self._median_sweep_count = int(median_sweep_count)
         self._is_multi_device = base_config.is_multi_device
         self._manual_multi_device_capture = self._is_multi_device and kind in MULTI_DEVICE_MANUAL_CAPTURE_KINDS
         self._combos = (
@@ -196,16 +202,23 @@ class MultiRadarSequentialCaptureSession:
                 self._radar.configure(variant.config.radar.sweep)
                 if self._base_config.runtime.settling_ms > 0:
                     time.sleep(self._base_config.runtime.settling_ms / 1000.0)
-                collection = self._radar.acquire_collection(collection_id=1)
-                if not collection.traces:
-                    raise RuntimeError(f"Multi-device variant {variant.display_name} returned no traces")
+                collections: list[SweepCollection] = []
+                for _ in range(self._median_sweep_count):
+                    collection = self._radar.acquire_collection(collection_id=1)
+                    if not collection.traces:
+                        raise RuntimeError(
+                            f"Multi-device variant {variant.display_name} returned no traces"
+                        )
+                    collections.append(collection)
                 if self._manual_multi_device_capture:
-                    trace = select_trace_for_combo(collection, combo)
+                    per_sweep_traces = [select_trace_for_combo(collection, combo) for collection in collections]
+                    trace = combine_traces_via_median(per_sweep_traces)
                     pending_traces_by_radar_key[variant.radar_key] = [trace]
                     display_traces.append(trace)
                 else:
-                    pending_traces_by_radar_key[variant.radar_key] = list(collection.traces)
-                    display_traces.append(collection.traces[-1])
+                    combined_collection = combine_collections_via_median(collections)
+                    pending_traces_by_radar_key[variant.radar_key] = list(combined_collection.traces)
+                    display_traces.append(combined_collection.traces[-1])
                 variant_labels.append(variant.display_name)
         else:
             assert self._input_switch is not None
@@ -219,13 +232,18 @@ class MultiRadarSequentialCaptureSession:
                 self._radar.configure(variant.config.radar.sweep)
                 if self._base_config.runtime.settling_ms > 0:
                     time.sleep(self._base_config.runtime.settling_ms / 1000.0)
-                sweep = self._radar.acquire()
-                trace = TraceData(
-                    combo=ComboKey(input_pos=combo.input, output_pos=combo.output),
-                    frequency_hz=np.asarray(sweep.x, dtype=np.float32),
-                    s11=np.asarray(sweep.trace("s11"), dtype=np.complex64),
-                    s21=np.asarray(sweep.trace("s21"), dtype=np.complex64),
-                )
+                sweep_traces: list[TraceData] = []
+                for _ in range(self._median_sweep_count):
+                    sweep = self._radar.acquire()
+                    sweep_traces.append(
+                        TraceData(
+                            combo=ComboKey(input=combo.input, output=combo.output),
+                            frequency_hz=np.asarray(sweep.x, dtype=np.float32),
+                            s11=np.asarray(sweep.trace("s11"), dtype=np.complex64),
+                            s21=np.asarray(sweep.trace("s21"), dtype=np.complex64),
+                        )
+                    )
+                trace = combine_traces_via_median(sweep_traces)
                 pending_traces_by_radar_key[variant.radar_key] = [trace]
                 display_traces.append(trace)
                 variant_labels.append(variant.display_name)
diff --git a/python_app/workflows/reference_workflow.py b/python_app/workflows/reference_workflow.py
index 53c8b2c..6785aee 100644
--- a/python_app/workflows/reference_workflow.py
+++ b/python_app/workflows/reference_workflow.py
@@ -5,16 +5,26 @@ from __future__ import annotations
 from python_app.models.dataset_model import SweepCollection
 from python_app.models.run_config_model import RunConfigModel
 from python_app.storage.npz_store import NpzStore
-from python_app.workflows.sequential_capture_workflow import SequentialCaptureSession
+from python_app.workflows.sequential_capture_workflow import (
+    DEFAULT_CALIBRATION_MEDIAN_SWEEP_COUNT,
+    SequentialCaptureSession,
+)
 
 
 def capture_reference_set(
     config: RunConfigModel,
     set_name: str,
     store: NpzStore,
+    *,
+    median_sweep_count: int = DEFAULT_CALIBRATION_MEDIAN_SWEEP_COUNT,
 ) -> tuple[str, SweepCollection]:
     """Capture all switch combinations and persist them as reference set."""
-    session = SequentialCaptureSession(config=config, kind="s21_reference", set_name=set_name)
+    session = SequentialCaptureSession(
+        config=config,
+        kind="s21_reference",
+        set_name=set_name,
+        median_sweep_count=median_sweep_count,
+    )
     try:
         session.open()
         while not session.is_complete():
diff --git a/python_app/workflows/sequential_capture_workflow.py b/python_app/workflows/sequential_capture_workflow.py
index 3d6caf4..d69e2af 100644
--- a/python_app/workflows/sequential_capture_workflow.py
+++ b/python_app/workflows/sequential_capture_workflow.py
@@ -16,6 +16,7 @@ from python_app.models.run_config_model import ComboModel, RunConfigModel
 from python_app.storage.npz_store import NpzStore, radar_key_from_config
 
 MULTI_DEVICE_MANUAL_CAPTURE_KINDS = frozenset({"s21_calibration", "s11_open", "s11_short", "s11_load"})
+DEFAULT_CALIBRATION_MEDIAN_SWEEP_COUNT = 5
 
 
 @dataclass(slots=True)
@@ -36,16 +37,26 @@ class SequentialCaptureState:
 class SequentialCaptureSession:
     """Manage hardware and switch stepping for full combo capture sequence."""
 
-    def __init__(self, config: RunConfigModel, kind: str, set_name: str) -> None:
+    def __init__(
+        self,
+        config: RunConfigModel,
+        kind: str,
+        set_name: str,
+        *,
+        median_sweep_count: int = 1,
+    ) -> None:
         """Create capture session for one preprocess asset set."""
         if kind not in {"s21_calibration", "s21_reference", "s11_open", "s11_short", "s11_load", "s11_reference"}:
             raise RuntimeError(f"Unsupported capture kind: {kind}")
         if not set_name:
             raise RuntimeError("Set name is required")
+        if int(median_sweep_count) < 1:
+            raise RuntimeError("median_sweep_count must be >= 1")
 
         self._config = config
         self._kind = kind
         self._set_name = set_name
+        self._median_sweep_count = int(median_sweep_count)
         self._is_multi_device = config.is_multi_device
         self._manual_multi_device_capture = self._is_multi_device and kind in MULTI_DEVICE_MANUAL_CAPTURE_KINDS
         self._combos = (
@@ -154,18 +165,23 @@ class SequentialCaptureSession:
             raise RuntimeError("Capture session is already complete")
 
         if self._is_multi_device:
-            collection = self._radar.acquire_collection(collection_id=1)
-            if not collection.traces:
-                raise RuntimeError("Multi-device capture returned no traces")
+            collections: list[SweepCollection] = []
+            for _ in range(self._median_sweep_count):
+                collection = self._radar.acquire_collection(collection_id=1)
+                if not collection.traces:
+                    raise RuntimeError("Multi-device capture returned no traces")
+                collections.append(collection)
             if self._manual_multi_device_capture:
-                trace = select_trace_for_combo(collection, combo)
+                per_sweep_traces = [select_trace_for_combo(collection, combo) for collection in collections]
+                trace = combine_traces_via_median(per_sweep_traces)
                 self._traces.append(trace)
                 self._next_index += 1
                 return trace
 
-            self._traces.extend(collection.traces)
+            combined_collection = combine_collections_via_median(collections)
+            self._traces.extend(combined_collection.traces)
             self._next_index = len(self._combos)
-            return collection.traces[-1]
+            return combined_collection.traces[-1]
 
         assert self._input_switch is not None
         assert self._output_switch is not None
@@ -174,13 +190,18 @@ class SequentialCaptureSession:
         if self._config.runtime.settling_ms > 0:
             time.sleep(self._config.runtime.settling_ms / 1000.0)
 
-        sweep = self._radar.acquire()
-        trace = TraceData(
-            combo=ComboKey(input_pos=combo.input, output_pos=combo.output),
-            frequency_hz=np.asarray(sweep.x, dtype=np.float32),
-            s11=np.asarray(sweep.trace("s11"), dtype=np.complex64),
-            s21=np.asarray(sweep.trace("s21"), dtype=np.complex64),
-        )
+        sweep_traces: list[TraceData] = []
+        for _ in range(self._median_sweep_count):
+            sweep = self._radar.acquire()
+            sweep_traces.append(
+                TraceData(
+                    combo=ComboKey(input=combo.input, output=combo.output),
+                    frequency_hz=np.asarray(sweep.x, dtype=np.float32),
+                    s11=np.asarray(sweep.trace("s11"), dtype=np.complex64),
+                    s21=np.asarray(sweep.trace("s21"), dtype=np.complex64),
+                )
+            )
+        trace = combine_traces_via_median(sweep_traces)
         self._traces.append(trace)
         self._next_index += 1
         return trace
@@ -203,8 +224,8 @@ class SequentialCaptureSession:
         expected_combo = self._combos[self._next_index - 1]
         removed_trace = self._traces[-1]
         if (
-            int(removed_trace.combo.input_pos) != int(expected_combo.input)
-            or int(removed_trace.combo.output_pos) != int(expected_combo.output)
+            int(removed_trace.combo.input) != int(expected_combo.input)
+            or int(removed_trace.combo.output) != int(expected_combo.output)
         ):
             raise RuntimeError("Capture session state is inconsistent; last trace does not match rewind combo")
         self._next_index -= 1
@@ -259,8 +280,94 @@ def select_trace_for_combo(collection: SweepCollection, combo: ComboModel) -> Tr
     """Return the trace matching a virtual combo from a full multi-device capture."""
     for trace in collection.traces:
         if (
-            int(trace.combo.input_pos) == int(combo.input)
-            and int(trace.combo.output_pos) == int(combo.output)
+            int(trace.combo.input) == int(combo.input)
+            and int(trace.combo.output) == int(combo.output)
         ):
             return trace
     raise RuntimeError(f"Multi-device capture is missing trace for input={combo.input}, output={combo.output}")
+
+
+def combine_traces_via_median(traces: list[TraceData]) -> TraceData:
+    """Return one trace whose S11/S21 are the per-point median of the inputs.
+
+    A single-element input is returned unchanged. With multiple inputs, the real
+    and imaginary parts of each complex sample are medianed independently so a
+    single bad sweep (e.g. an outlier with random phase) is rejected without
+    corrupting the saved calibration trace.
+    """
+    if not traces:
+        raise RuntimeError("Cannot combine empty sweep list")
+    if len(traces) == 1:
+        return traces[0]
+
+    first = traces[0]
+    combo = first.combo
+    point_count = first.frequency_hz.size
+    for index, trace in enumerate(traces[1:], start=1):
+        if (
+            int(trace.combo.input) != int(combo.input)
+            or int(trace.combo.output) != int(combo.output)
+        ):
+            raise RuntimeError(
+                f"Median combine combo mismatch at sweep {index}: "
+                f"({trace.combo.input},{trace.combo.output}) "
+                f"vs ({combo.input},{combo.output})"
+            )
+        if trace.frequency_hz.size != point_count:
+            raise RuntimeError(
+                f"Median combine point-count mismatch at sweep {index}: "
+                f"{trace.frequency_hz.size} vs {point_count}"
+            )
+
+    s11_stack = np.stack([np.asarray(t.s11, dtype=np.complex64) for t in traces], axis=0)
+    s21_stack = np.stack([np.asarray(t.s21, dtype=np.complex64) for t in traces], axis=0)
+    s11_median = (
+        np.median(s11_stack.real, axis=0) + 1j * np.median(s11_stack.imag, axis=0)
+    ).astype(np.complex64)
+    s21_median = (
+        np.median(s21_stack.real, axis=0) + 1j * np.median(s21_stack.imag, axis=0)
+    ).astype(np.complex64)
+    return TraceData(
+        combo=ComboKey(input=int(combo.input), output=int(combo.output)),
+        frequency_hz=np.asarray(first.frequency_hz, dtype=np.float32),
+        s11=s11_median,
+        s21=s21_median,
+    )
+
+
+def combine_collections_via_median(collections: list[SweepCollection]) -> SweepCollection:
+    """Combine multi-device matrix captures into one collection with per-combo medians."""
+    if not collections:
+        raise RuntimeError("Cannot combine empty collection list")
+    if len(collections) == 1:
+        return collections[0]
+
+    reference = collections[0]
+    expected_combos = [(trace.combo.input, trace.combo.output) for trace in reference.traces]
+    medianed_traces: list[TraceData] = []
+    for combo_index, (input_pos, output_pos) in enumerate(expected_combos):
+        per_sweep_traces: list[TraceData] = []
+        for collection_index, collection in enumerate(collections):
+            if combo_index >= len(collection.traces):
+                raise RuntimeError(
+                    f"Median collections have mismatched trace counts at sweep {collection_index}"
+                )
+            trace = collection.traces[combo_index]
+            if (
+                int(trace.combo.input) != int(input_pos)
+                or int(trace.combo.output) != int(output_pos)
+            ):
+                raise RuntimeError(
+                    f"Median collections trace order mismatch at sweep {collection_index}, "
+                    f"combo index {combo_index}"
+                )
+            per_sweep_traces.append(trace)
+        medianed_traces.append(combine_traces_via_median(per_sweep_traces))
+
+    return SweepCollection(
+        collection_id=int(reference.collection_id),
+        monotonic_ns=int(reference.monotonic_ns),
+        traces=medianed_traces,
+        capture_start_ns=int(reference.capture_start_ns),
+        capture_end_ns=int(reference.capture_end_ns),
+    )